Systems, methods, and media for presenting medical imaging data in an interactive virtual environment reality are provided. In some embodiments, a system comprises a head mounted display (HMD) that: determines that a transparent 3D object overlaps a 3D model of a portion of anatomy based on a medical imaging scan； sets values for pixels corresponding to portions of the 3D model not occluded by the transparent object by performing a shading operation； sets values for pixels corresponding to portions of the 3D model at the boundary of the transparent object to intensity values taken from the medical imaging data； displays the 3D model with an exterior surface shaded to evoke a 3D object, and internal surfaces at the boundaries of the transparent object not shaded to preserve details embedded in the medical imaging data.
